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alexlancaster / pypop

PyPop: Python for Population Genomics
http://pypop.org
GNU General Public License v2.0
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Use standard `.tsv` suffix in place of `.dat`, keep track of generated files #126

Closed alexlancaster closed 1 year ago

alexlancaster commented 1 year ago

@rsingle & @sjmack: In this PR I have changed the output of the generation of TSV files in both pypop and popmeta to use the standard .tsv rather than .dat throughout. I think this will make it more obvious what the format of these files are. I have also dropped any specific mention of these being "R files", since TSV can be used via any dataviz engine.

I've also added a new --prefix-tsv option to both scripts allow all generated files to include a prefix, so that outputs can be created like prefix-1-locus-summary.tsv. Along with the existing -o to generate TSV file in a separate directory, this should help prevent overwriting of older analyses. I've also made the programs smarter about keeping track of which TSV files are generated when processing in batches.

Lastly, I've added some unit tests and updated the docs a bit to include these new options.

Let me know what you think, I'd like to get this in the beta release.

alexlancaster commented 1 year ago

OK, since I didn't hear any negative feedback on the change, I'm going to merge to main.